The West Nile virus (WNV) is a mosquito-born flaviviruses that can cause acute neurological illness with up to 30% mortality and permanent neurological disabilities in the survivors. The virus has been identified by the National Institute of Allergy and Infectious Diseases (NIAID) as a category B bioterrorism agent. There is currently no effective treatment for WNV infection.
Flaviviruses are small (40-60 nm) enveloped viruses with a single-stranded positive-sense RNA genome that is approximately 11 kb long. The genome encodes a long polyprotein and is flanked by two nontranslated regions (5′ and 3′ NTR). The 3000 amino acid polyprotein is cleaved into three structural proteins, the core protein C, the premembrane protein (prM) and the envelope protein (E) and seven nonstructural (NS) viral proteins, NS1-NS5. Several regions in the viral genome are highly conserved among the different strains within a species as well as across the different flaviviral species. These include, in particular, the region coding for the cd loop of the envelope protein, and the region coding for the nonstructural proteins NS3 and NS5. All flaviviruses share two short conserved RNA sequences near the 3′ end of the RNA genome. For mosquito-borne flaviviruses, such as WNV, the elements are the 26 nt CS1 and the 24 nt CS2. Part of CS1 is complementary to a conserved sequence near the 5′ end of the genome in the region encoding the capsid protein which is referred to as 5′CS. Base pairing of these sequences is thought to be involved in cyclization of the viral genome.
Double-stranded RNA molecules (dsRNA) have been shown to block gene expression in a highly conserved regulatory mechanism known as RNA interference (RNAi). WO 99/32619 (Fire et al.) discloses the use of a dsRNA of at least 25 nucleotides in length to inhibit the expression of genes in C. elegans. dsRNA has also been shown to degrade target RNA in other organisms, including plants (see, e.g., WO 99/53050, Waterhouse et al.; and WO 99/61631, Heifetz et al.), Drosophila (see, e.g., Yang, D., et al., Curr. Biol. (2000) 10:1191-1200), and mammals (see WO 00/44895, Limmer; and DE 101 00 586.5, Kreutzer et al.). This natural mechanism has now become the focus for the development of a new class of pharmaceutical agents for treating disorders that are caused by the aberrant or unwanted regulation of an RNA.